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- PDB-1n7b: RIP-Radiation-damage Induced Phasing -

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Basic information

Entry
Database: PDB / ID: 1n7b
TitleRIP-Radiation-damage Induced Phasing
ComponentsRNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
KeywordsDNA / RNA
Function / homology: / SPERMINE / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIP - Radiation-damage Induced Phasing / Resolution: 1.4 Å
AuthorsRavelli, R.B.G. / Leiros, H.-K.S. / Pan, B. / Caffrey, M. / McSweeney, S.
CitationJournal: Structure / Year: 2003
Title: Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures
Authors: Ravelli, R.B.G. / Leiros, H.-K.S. / Pan, B. / Caffrey, M. / McSweeney, S.
History
DepositionNov 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
B: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
C: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
D: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
E: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
F: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
G: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
H: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,71719
Polymers15,9618
Non-polymers75711
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.247, 51.154, 70.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid
RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')


Mass: 1995.093 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: The RNA hexamer UGAGGU where the 2nd G was replaced by a C8-brominated Gd was phased using radiation damage on the highly susceptible Br-C8 bond.
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR ...Details: 1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1RNA11
2sodium cacodylate11
3spermine tetrachloride11
4KCl11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDDetailsChemical formula
11 mM1dropsingle strand
220 mM1droppH6.0
35 mM1drop
432 mM1dropKCl
52 %(v/v)1drop
625 %1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2002
RadiationMonochromator: diamond(111) and Ge(200) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 22939 / Num. obs: 22939 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.25 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.99
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3438 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / Redundancy: 4.2 %
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 98.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
ProDCdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
REFMAC5.1.24refinement
XDSdata scaling
RefinementMethod to determine structure: RIP - Radiation-damage Induced Phasing
Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 0.986 / SU ML: 0.039
Isotropic thermal model: The DNA/RNA and K-atoms were refined anisotropically, the spermine and waters isotropic
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The model was built and refined against the data set collected before the "X-ray burn". Afterwards, the model was refined for some additional cycles against the data set that was collected ...Details: The model was built and refined against the data set collected before the "X-ray burn". Afterwards, the model was refined for some additional cycles against the data set that was collected after the "X-ray burn". No manual adjustments were made, resulting in strong negative densities in the Fo-Fc difference map on X-ray susceptible sites, such as the Br-atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.19949 1148 5 %RANDOM
Rwork0.15216 ---
all0.15453 22939 --
obs0.15453 22939 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1024 31 181 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211171
X-RAY DIFFRACTIONr_angle_refined_deg1.93531778
X-RAY DIFFRACTIONr_chiral_restr0.1080.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02520
X-RAY DIFFRACTIONr_nbd_refined0.4120.2409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.222
X-RAY DIFFRACTIONr_scbond_it3.13131164
X-RAY DIFFRACTIONr_scangle_it3.8444.51778
X-RAY DIFFRACTIONr_rigid_bond_restr2.12821144
X-RAY DIFFRACTIONr_sphericity_free4.347517
X-RAY DIFFRACTIONr_sphericity_bonded5.79151016
LS refinement shellResolution: 1.4→1.476 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.286 155
Rwork0.194 3104
Refinement
*PLUS
Highest resolution: 1.42 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.48 Å

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